Chapter 9, Molecular Structure of DNA and RNA
Chapter 9, Molecular Structure of DNA and RNA
Chapter 9, Molecular Structure of DNA and RNA
Introduction to
DNA and RNA
(Chapter 09)
Slides 1-25; 35-48; 54-57
On your own:
Slides 26-34; 49-53; 58-62
1
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INTRODUCTION
Genetics: Study of the structure, function,
transmission of genes
Only living organisms have genes
To understand genetics, we will start with the
question: What is Life?
Characteristics shared by all living forms but not by
non-living forms
UNIVERSE
LIFE (GENES)
(entropy)
(negative entropy)
MOLECULAR GENETICS
Chapter 9 examines the genetic material in detail:
molecular genetics
The study of DNA structure and function at the
molecular level
R Rough
Unable to secrete a capsule
Produce colonies with a rough appearance
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10
Mouse survived
No living bacteria isolated from the mouses blood
Mouse died
Type IIIS bacteria recovered from the mouses blood
Mouse survived
No living bacteria isolated from the mouses blood
4. Inject mouse with live type IIR + heat-killed type IIIS cells
Mouse died
Type IIIS bacteria recovered from the mouses blood
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11
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Dead
type S
After
several
days
Mouse died
After
several
days
Mouse survived
After
several
days
Mouse survived
After
several
days
Mouse died
Figure 9.1
12
13
14
The Experiments of
Avery, MacLeod and McCarty
Avery, MacLeod and McCarty realized that Griffiths
observations could be used to identify the genetic material
They carried out their experiments in the 1940s
At that time, it was known that DNA, RNA, proteins and
carbohydrates are the major constituents of living cells
They prepared cell extracts from type IIIS cells and purified
each type of macromolecule
Only the extract that contained purified DNA was able to convert
type IIR bacteria into type IIIS
Treatment of the DNA extract with RNase or protease did not
eliminate transformation
Treatment with DNase did
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15
Figure 9.2
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Type R
cells
Type S
DNA
extract
Type R
cells
Mix
Type S
DNA
extract
+
DNase
Type R
cells
Mix
Type S
DNA
extract
+
RNase
Type R
cells
Mix
Type R
cells
Type S
DNA
extract
+
protease
Mix
Allow sufficient time for the DNA to be taken up by the type R bacteria. Only a small percentage of the type R bacteria will be transformed to type S.
Add an antibody that aggregates type R bacteria (that have not been transformed). The aggregated bacteria are removed by gentle centrifugation.
Plate the remaining bacteria on petri plates. Incubate overnight.
Transformed
Transformed
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Transformed
16
Figure 9.3
It is relatively simple
since its composed of
only two
macromolecules
DNA
(inside the
capsid head)
Inside the
capsid
Head
Sheath
Made up
of protein
Tail fiber
Base plate
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17
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Phage binds to host cell.
Capsid
Genetic material
Bacterial
cell wall
Bacterial
chromosome
Figure 9.4
The expression of
phage genes leads
to the synthesis of
phage components.
Life cycle of
bacteriophage T2
18
19
9-14
The Hypothesis
Only the genetic material of the phage is injected
into the bacterium
Isotope labeling will reveal if it is DNA or protein
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20
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Experimental level
Conceptual level
1.Grow bacterial cells. Divide into
two flasks.
Suspension of
E. coli cells
S-labeled
protein capsid
35
P-labeled
DNA
32
S-labeled
T2 phage
35
P-labeled
T2 phage
32
Figure 9.5
Supernatant
with
unlabeled
empty phage
Pellet with
32
P-labeled
DNA in
infected
E. coli cells
Bacterial cell
Viral genetic
material
Sheared empty
phage (labeled)
Bacterial
cell
Viral
genetic
material
(labeled)
Sheared
empty
phage
Sheared empty
phages (labeled)
Sheared
empty
phages
(unlabeled)
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21
The Data
Total isotope in supernatant (%)
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100
80
Extracellular 35S
80%
Blending removes 80%
of 35S from E. coli cells.
Extracellular 32P
35%
Most of the 32P (65%)
remains with intact
E. coli cells.
60
40
20
0
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100
80
Extracellular 35S
80%
Blending removes 80%
of 35S from E. coli cells.
Extracellular 32P
35%
Most of the 32P (65%)
remains with intact
E. coli cells.
60
40
20
0
These results suggest that DNA is injected into the bacterial cytoplasm
during infection
Data is not conclusive since less than 100% of the DNA or protein
ended up in the cell or supernatant
Data is consistent with the hypothesis that DNA is the genetic
material
23
9-18
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24
25
26
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Nucleotides
A
TC
AA
TC
AA
TC
AAT
Single strand
C
G
C A
T GT
T A
A
G T
A C
GA
T
C A
T GT
T A
A
Double helix
Figure 9.6
Three-dimensional structure
27
Nucleotides
A phosphate group
A pentose sugar
A nitrogenous base
28
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Bases
Phosphate group
Sugars
5
HOCH2
4
O
CH3
1N
H
3
HO
OH
N
H
3N
2
Adenine (A)
OH
1N
4
1
3N
2
NH 2
H
NH2
HOCH2
Figure 9.7
HO
O
Pyrimidines
(single ring)
NH2
OH
Purines
(double ring)
5
6
4
1
3N
2
H
Guanine (G)
Cytosine (C)
29
9-24
A, G, C or U
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O
O P
Base
O
O
Phosphate
CH2
5
4
H
3
H
2
OH
H
Deoxyribose
Base
O
O
Phosphate
CH2
H
3
O
H
2
OH
OH
Ribose
30
Example
Adenine + ribose = Adenosine
Adenine + deoxyribose = Deoxyadenosine
Example
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
31
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Adenosine triphosphate
Adenosine diphosphate
Adenosine monophosphate
Adenosine
Adenine
Phosphoester bond
NH2
H
O
O
P
O
O
O
O
O
N
O
Phosphate groups
Phosphates are
attached here
Figure 9.9
CH2
5
4
HO
Ribose
N
Base always
attached here
OH
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32
33
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Backbone
Bases
O
CH3
H
O
O
CH2
5
4
H
H
O
1
H
2
H
H
Phosphodiester
linkage
Thymine (T)
NH2
N
H
N
O
O
CH2
5
4
H
H
1
H
2
H
H
NH2
H
O
P
Adenine (A)
CH2
5
4
H
H
Cytosine (C)
O
O
1
H
2
H
H
Guanine (G)
O
N
H
N
Single
nucleotide
CH2
5
O
4
H
Phosphate H
3
OH
Figure 9.10
NH2
O
1
H
2
H
H
Sugar (deoxyribose)
34
Linus Pauling
Rosalind Franklin and Maurice Wilkins
Erwin Chargaff
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Linus Pauling
-helix
N C C
O
N
HO
O N
H
N
C
H
N
C
Carbonyl
oxygen
Amide
hydrogen
O N
O
Hydrogen
bond
C
H
O
N
N
C
Figure 9.11
36
Rosalind Franklin
X rays diffracted
by DNA
Wet DNA fibers
X-ray beam
Figure 9.12b
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37
Rosalind Franklin
Helical
More than one strand
10 base pairs per complete turn
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38
39
The Hypothesis
An analysis of the base composition of DNA in
different species may reveal important features
about the structure of DNA
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40
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y
Conceptual level
Experimental level
Solution of
1. For each type of cell, extract the
chromosomal
chromosomal material. This can be extract
done in a variety of ways, including the
use of high salt, detergent, or mild alkali
treatment. Note: The chromosomes
contain both DNA and protein.
DNA +
proteins
Protease
DNA
Acid
Figure 9.13
AA A
A A
C
C C C CC C
G
G G GG G
TT
Individual
bases
G
T
41
The Data
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42
43
44
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Base
Base
Sugar
Sugar
O
Base
O
P
O
Sugar
Mg2+
Base
P
O
O
Sugar
Figure 9.14
45
ie., A to A, T to T, C to C, and G to G
46
These were consistent with all known data about DNA structure
47
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Figure 9.15
48
49
2. Base stacking
Within the DNA, the bases are oriented so that the flattened
regions are facing each other
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50
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2 nm
Key Features
5 P 3
S P
P
A S
G
G
S
C
P S
P
P
S
S
T
P
Figure 9.16
C
P
O P
N
O
3 end
HO
HH
H
O
CH2
H
NH2
H
N
P S
O P
CH2
H
H H
N
HH
CH2 O P
N
O
H2N
CH3
O
H
G S
H2N
H H
N
H H
H
O
CH2 O P O
O
H N
O P
One nucleotide
0.34 nm
O
O
CH2
H
H
OH
H2N
N H
NH2
3 end
S
CH2 O P
O
C P
P S
C
P S
PS
P
S C
S
CH2
NH2
G
A
O P O
CH3
O
O
T
A
P
G
S
P
5 end
One complete
turn 3.4 nm
H
N
H H
H
H
CH2 O P
O
5 end
3
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51
1. Major groove
2. Minor groove
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Minor
groove
Minor
groove
Major
groove
Major
groove
Laguna Design/Photo Researchers
Figure 9.17
53
Refer to 9.20
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55
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Radial loops
(300 nm in diameter)
Metaphase
chromosome
30 nm fiber
Nucleosomes
(11 nm in diameter)
DNA
(2 nm in diameter)
Histone
protein
DNA wound
around histone
proteins
Each chromatid
(700 nm in diameter)
Figure 9.20
56
57
58
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Backbone
Bases
O
H
O
O
P
O
5
4
CH2
H
Uracil (U)
O
1
H
2
OH
Phosphodiester
linkage
NH2
N
H
N
O
O
P
O
5
4
CH2
H
Adenine (A)
O
1
H
2
OH
NH2
H
O
O
5
4
CH2
Cytosine (C)
1
H
Guanine
(G)
2
OH
H
N
RNA
nucleotide
Phosphate
Figure 9.21
5
4
CH2
H
NH2
3
OH
Sugar (ribose)
1
H
2
OH
59
A to U and C to G
Are right-handed
Have the A form with 11 to 12 base pairs per turn
60
Complementary regions
Held together by
hydrogen bonds
Figure 9.22
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U
U A
A
A U
U A
G C
C G
C G
C
A
A U
(a) Bulge loop
U
G
C G
C G
C
U A
C G
G C A A G
G
C
U U C
A
C
C C G A A
G G
C U U
G C
A U
A U
C G
Non-complementary regions
Have bases projecting away
from double stranded regions
C G
G C
A U
A U
C G
C G
C G
A U
U A
A
G
G C
A U
C
U
A
G
G
U
C A
C
G G
A
C C G U
(d) Stem-loop
Also called
hair-pin
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Double helix
Many factors
contribute to the
tertiary structure of
RNA
5 end
Molecule contains
single- and doublestranded regions
For example
Base-pairing and
base stacking within
the RNA itself
Interactions with
ions, small
molecules and large
proteins
3 end
(acceptor
site)
Double helix
These spontaneously
fold and interact to
produce this 3-D
structure
Anticodon
(a) Ribbon model
Figure 9.23
62
Animations
63
64
65